Also have consistently been having issues where a program thrown into the background is immediately killed.
I've messed around with the Overcharge script in the past (maybe that did something), I've used motomizer, Loki's de-blur script. I've also added the modified app widget picker and removed a few Blur items.
I decided to sbf to 198_7 and start over from scratch, I've only installed a few new programs (google Reader, TB, Rom toolbox, Solid file Explorer, ES File explorer) and uninstalled the Sprint apps that are easy to remove (Nascar, Telenav, etc). My BT headset works while the phone is in the cardock now (yay) but I am still having the slow / laggy response in the UI.
A good example of the lag is when I unlock the phone. Remember, at this point I am near total stock, only with root. When I slide to unlock from the screen, there is a noticable delay before I get the homescreen. I watched one of qbking77's videos about restoring via SBF last night and on his demo, when he would unlock his photon it would "immediately" show the homescreen.
TLDR: Is it possible to have a problem re: performance separate from the image on the phone, something in the hardware. Totally subjective but something doesn't seem right and I've reset it as much as I can.